Hi Martin,
You are great.I have changed the lines of collection.cpp,MCPB is ok now
but minimization with ligand,the structure of the ligand(CA1) changed so
worsely as before.
After wrote parmtop and inpcrd of 3H68_OH_mcpb.pdb,I run "charge
model",it shown -3.999940,I also run "charge model.CA1",it shown
-0.656100,could the charge of CA1 is not zero to be a problem?
I copied the prep information of CA1 from the 3H68_OH_chg2.prep file,and
run minimization on the ligand by itself,it's structure still deform.How
could I solve this problem.
Best Regards
JiYuan
于 2011年12月22日 23:54, Martin Peters 写道:
> Hi JiYuan,
>
> On 22 Dec 2011, at 14:06, JiYuan Liu wrote:
>
>> Hi Martin,
>>
>> I am sorry I could not clear express my mean about the parmtop of 3H68 in the previous emails,You may misunderstand my meaning.I would tell you this situation follow:
>>
>> Although MCPB can't get the correct metal center before change the lines of collection.cpp,I modified the bond information in 3H68_OH.leaprc and the residue name in 3H68_OH_mcpb.pdb by my hand,I ensured the correctness of them before I used tleap to generate the parmtop of 3H68.I think these two files make no difference as that you sent to me.
>>
>> Would you like to help me to do a test:you could use these files to generate the parmtop and inpcrd of 3H68_OH_mcpb.pdb,and you can use the min.in that in this attachment to run a short minimization,then you can see the structure of the small molecule change so worsely,this is my actual problem.
> Yes, I can confirm that there is a problem with the ligand after minimization. Did you run minimization on the ligand by itself?
>
>> Please tell me how to only recompile mtkpp.Could you tell me why I need to recalculate the Side Chain Model Optimization/Frequency Calculation and Large Model Charge Calculation after I changed the lines of collection.cpp follow your instruction.
> cd $AMBERHOME/AmberTools/src/mtkpp
> make ; make install
>
> I didn't say you had to redo the side chain / freq calcs after the changes to collection.cpp but you may have to if the minimization doesn't work.
>
> Look at the charges and other parameters in the prep file to see if they make sense. If you see problems it might be best to redo some steps after applying the patch.
>
> Regards,
> Martin
>
>
>> Best Regard
>>
>> JiYuan
>>
>>
>> 于 2011年12月22日 21:08, Martin Peters 写道:
>>> Hi JiYuan,
>>>
>>> On 22 Dec 2011, at 12:41, JiYuan Liu wrote:
>>>
>>>> Hi Martin,
>>>>
>>>> Thank you very much.I have looked for the attachments,it looks fine that
>>>> can get the metal center correctly.Because I added the intel compilers
>>>> and cuda technology to accelerate the calculation of Amber,it took me so
>>>> long time to
>>>>
>>>> recompile it for the bugfix25 in the recent time.I would make sure that
>>>> if I change the lines of collection.cpp,could it fix those previous
>>>> problems below:
>>> All you need to do is recompile mtkpp not the whole package. Should take seconds.
>>>
>>>> 1. 3H68_OH_resNames.bcl,it can write pdb with new residue names like
>>>> HD1,HD2,CA1 et al. now?
>>> Yes, I sent you the result.
>>>
>>>> 2. When I runed the min.in with the parmtop that be generated by MCPB,
>>>> the two ZN ions is stable after the minimization, but the ligand is
>>>> deformed very serious.Does the ligand become stable now?
>>> For now don't use the prmtop file from MCPB. Create a prmtop from leap using the leaprc file i sent you.
>>>
>>>> By the way if I change the lines of collection.cpp and recompile
>>>> ambertools,could I recalculate the Side Chain Model
>>>> Optimization/Frequency Calculation and Large Model Charge Calculation?
>>> I don't see why not.
>>>
>>> Regards,
>>> Martin
>>>
>>>> Best Regards
>>>>
>>>> JiYuan
>>>>
>>>>
>>>>
>>>> ? 2011?12?22? 18:38, Martin Peters ??:
>>>>> Dear JiYuan,
>>>>>
>>>>> Please find attached an updated 3H68_OH_mcpb.pdb file with the metal center correctly found.
>>>>>
>>>>> In $AMBERHOME/AmberTools/src/mtkpp/src/molecule/collection.cpp
>>>>>
>>>>> changing the lines (around line 230):
>>>>> metalDonorDists["Zn:SER"] = 1.14;
>>>>> and
>>>>> metalDonorDists["Zn:S"] = 1.14;
>>>>>
>>>>> to
>>>>> metalDonorDists["Zn:SER"] = 2.14;
>>>>> and
>>>>> metalDonorDists["Zn:S"] = 2.14;
>>>>>
>>>>> fixes the problem. You can do the same and recompile.
>>>>>
>>>>> This may appear strange but when a ligand oxygen is bound to a metal I use the Serine-metal distance as a reference.
>>>>> The 2.14A number was problematic in other systems. I will implement a system to allow these parameters to be changed from a file.
>>>>>
>>>>> HTH,
>>>>> Martin
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 21 Dec 2011, at 02:24, JiYuan Liu wrote:
>>>>>
>>>>>> Hi Martin,
>>>>>> I have attached them,you could download.
>>>>>> Best Regards
>>>>>> JiYuan
>>>>>>
>>>>>> ? 2011?12?20? 21:31, Martin Peters ??:
>>>>>>> Hi JiYuan,
>>>>>>>
>>>>>>> Two final files are required:
>>>>>>> caparm.xml and calib.xml
>>>>>>>
>>>>>>> Regards,
>>>>>>> Martin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 20 Dec 2011, at 13:04, JiYuan Liu wrote:
>>>>>>>
>>>>>>>> Hi Martin,
>>>>>>>> I have attached them,you could download them to have a test.I am waitting for your reply.Thank you.
>>>>>>>> Best Regards
>>>>>>>> JiYuan
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ? 2011?12?20? 17:08, Martin Peters ??:
>>>>>>>>> Hi JiYuan,
>>>>>>>>>
>>>>>>>>> Please send us all the files necessary to reproduce the problem:
>>>>>>>>>
>>>>>>>>> 3H68_OH_resNames.bcl
>>>>>>>>> 3H68_OH_settings.bcl
>>>>>>>>> 3H68_OH_params_fc_md.xml
>>>>>>>>> 3H68_OH_chg2.xml
>>>>>>>>> 3H68_OH_stdMol.xml
>>>>>>>>> 3H68_OH_fixed_H.pdb
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>> Martin
>>>>>>>>>
>>>>>>>>> On 20 Dec 2011, at 02:37, JiYuan Liu wrote:
>>>>>>>>>
>>>>>>>>>> Hi Ben,
>>>>>>>>>> I have updated MTK++ and MCPB patch released,but the situation changed
>>>>>>>>>> more worse,so I recoveried my Amber11 and ambertools11.
>>>>>>>>>> By the way,I have attached all of files in the maillist with the title "The
>>>>>>>>>> charge is wrong when the ligand together with the large model in MCPB",you
>>>>>>>>>> could help me to test it,I want to know 3 things which I can not solve.
>>>>>>>>>> 1. a command findMetalCenters in 3H68_OH_resNames.bcl,when I run this BCL
>>>>>>>>>> script,I can' t get the complete bond informations between atom to atom in
>>>>>>>>>> 3H68_OH.leaprc;
>>>>>>>>>> 2. in 3H68_OH_resNames.bcl,I checked one of the results with
>>>>>>>>>> 3H68_OH_mcpb.pdb,it can't Write pdb with new residue names,the residues
>>>>>>>>>> which are coordinated with ZN ions could not be change their original name
>>>>>>>>>> into the new name as HD1 AS1 et al.
>>>>>>>>>> You can refer to these from my attachments.
>>>>>>>>>> 3. When I runed the min.in with the parmtop that be generated by MCPB, the
>>>>>>>>>> two ZN ions is stable after the minimization, but the ligand is deformed
>>>>>>>>>> very serious.
>>>>>>>>>> I was very warried about these errors,please help me,thank you.
>>>>>>>>>> Best Regards
>>>>>>>>>> JiYuan
>>>>>>>>>> _______________________________________________
>>>>>>>>>> AMBER mailing list
>>>>>>>>>> AMBER.ambermd.org
>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Jiyuan Liu
>>>>>>>> Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
>>>>>>>> Northwest A&F University
>>>>>>>> Yangling, Shaanxi
>>>>>>>> China 712100
>>>>>>>> Phone: 86-29-87092190
>>>>>>>>
>>>>>>>> <3H68_OH_resNames.bcl><3H68_OH_settings.bcl><3H68_OH_params_fc_md.xml><3H68_OH_chg2.xml><3H68_OH_stdMol.xml><3H68_OH_fixed_H.pdb>_______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>> --
>>>>>> Jiyuan Liu
>>>>>> Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
>>>>>> Northwest A&F University
>>>>>> Yangling, Shaanxi
>>>>>> China 712100
>>>>>> Phone: 86-29-87092190
>>>>>>
>>>>>> <caparm.xml><calib.xml>_______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> --
>>>> Jiyuan Liu
>>>> Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
>>>> Northwest A&F University
>>>> Yangling, Shaanxi
>>>> China 712100
>>>> Phone: 86-29-87092190
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Jiyuan Liu
>> Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
>> Northwest A&F University
>> Yangling, Shaanxi
>> China 712100
>> Phone: 86-29-87092190
>>
>> <min.in>_______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jiyuan Liu
Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
Northwest A&F University
Yangling, Shaanxi
China 712100
Phone: 86-29-87092190
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 24 2011 - 03:00:03 PST
